Puzzle Village is the setting of Pokémon Puzzle League. When Ash receives a phone call from Professor Oak, telling him he'd been selected as a challenger of the Puzzle League Tournament, he and Pikachu race to Puzzle Village. It has nine locations: Puzzle University, Pokémon Center, Marathon, 2P Stadium, 1P Stadium, Prof. Oak's Labs, Spa Service, Time Zone, and Mimic Mansion.

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Locations in Puzzle Village

Puzzle University

The Puzzle University contains a series of challenge puzzles for the player to complete. The player is given a set of blocks and a specific number of moves. Using the number of moves displayed or less, the player's objective is to clear all of the blocks from the screen. The puzzles progressively get harder, branching out into 3-D puzzles and action puzzles, where the player is required to make moves while the blocks are still in the air.

The player can also create custom puzzles. Using a block-placing tool, they can place as many blocks as desired on the screen, and select a number of moves from 1 to 5. They can then test their puzzle to ensure that it is possible.

Pokémon Center

Run by Nurse Joy, the Pokémon Center is the "extras" menu. Here, the player can view records, character profiles, and change game and sound settings. One notable game setting is the ability to set the style of the blocks to be either gym badges or little colored shapes that make faces when defeated or cleared. Choosing the latter also causes opponents to speak whenever they make a combo or chain.

The records menu gives the battle records of each player as they have played the game. The profiles menu allows the player to select a character and see their artwork and their Pokémon as seen in the game.

Marathon

The marathon is an endless puzzle game. The player can choose between 2D and 3D, select the speed of the blocks (from 1-99), and select the level of difficulty (easy, normal, hard). The speed of the blocks will gradually increase thoughout the game, thereby making it progressively more difficult. The blocks stop moving whenever a combo or chain is made; when the blocks touch the top of the playing field, the game ends and the total number of combos and chains is tallied. Selecting "hard" mode initially will add a dark blue block that was not present before.

2P Stadium

The 2P Stadium is for two players. There are three options: 2P VS, Time Zone, and Spa Service. 2P VS is a standard best three out of five match. The first player whose blocks try to push on the ceiling loses. At the beginning of this and both other match styles, the players choose between 2D and 3D playing fields and choose their game level, ranked from 1-10. The speed of the blocks increases with each level. If the player is level 9 or 10, a dark blue block will be added to the other six as an extra challenge.

In Time Zone, two players compete to see who can score the most points in two minutes. Handicap points are available at the start of the match.

In Spa Service, a Clear Line is set to appear once a player gets far enough. The first player to get all of their blocks below this line is the winner.

All matches are best three out of five.

1P Stadium

The 1P Stadium is designed for one player to battle a series of computers. There are five levels: Easy, Normal, Hard, Very Hard, and Super Hard. In Easy mode, the player, playing as Ash Ketchum, battles Gary Oak, Brock, Misty, Lt. Surge, Erika, Koga, Sabrina, Blaine, Team Rocket, Tracey Sketchit, and Giovanni. In Normal mode, the Puzzle Elite is added: Ritchie, Lorelei, and Bruno. In Hard mode, the player battles all of these and Gary again at the end. In both Very Hard and Super Hard modes, upon defeating Gary, the player must battle Mewtwo and his clones. If the player loses to Mewtwo, they must re-battle Gary until they can beat him and Mewtwo consecutively.

In each mode, the computer players get progressively more difficult, until in Super Hard mode, they can move their blocks extremely fast and are difficult to beat.

Prof. Oak's Labs

Professor Oak teaches the player how to play the game. He has six tutorials: Controls, Basic 1, Basic 2, VS Rules 1, VS Rules 2, and 3D Rules. In each tutorial, he explains various aspects of playing the game.

Spa Service

This is the battle with Team Rocket. Posing as a spa service, they steal the player's Squirtle and Bulbasaur. The player then chases them through six stages. to advance to the next stage, the player must defeat them five times on the current stage by getting all of their blocks below the clear line, just as in Spa Service for two players. However, if any blocks touch the top of the field, the player must start over that particular match.

After the third round, Butch and Cassidy make an appearance. The player is given one shot to beat them. The screen moves much faster and the goal is to completely deplete the meter on the left-hand side of the screen. Once the meter is depleted, the game halts and the player moves to Round 4. If the player loses, they are not given another chance and move on to Round 4 anyway.

For Rounds 4-6, the field changes to 3D. The rules are the same, and, after Round 6, the player faces Giovanni. Unlike Butch and Cassidy, the player can face Giovanni over and over. The rules for Giovanni are the same as for Butch and Cassidy: deplete the meter on the side of the screen.

Before facing Giovanni, of course, Team Rocket goes blasting off again in a short clip.

Time Zone

In Time Zone, the player is given two minutes to rack up as many points as they can by exploiting combos and chains. The player can choose between 2D and 3D and set the block speed (from 1-50). There are also Easy, Normal, and Hard modes similar to those in the Marathon.

Mimic Mansion

The Mimic Mansion, run by Tracey Sketchit, outlines some of the finer points of playing. He offers demos, and a "mimic mode" in which the player repeats everything he does. There is also a "Super Easy" mode for practice.